Haplogroup DE (Y-DNA)
Encyclopedia
In human genetics
Human genetics
Human genetics describes the study of inheritance as it occurs in human beings. Human genetics encompasses a variety of overlapping fields including: classical genetics, cytogenetics, molecular genetics, biochemical genetics, genomics, population genetics, developmental genetics, clinical genetics,...

, Haplogroup DE is a human Y-chromosome DNA haplogroup. It is defined by the single nucleotide polymorphism
Single nucleotide polymorphism
A single-nucleotide polymorphism is a DNA sequence variation occurring when a single nucleotide — A, T, C or G — in the genome differs between members of a biological species or paired chromosomes in an individual...

 (SNP) mutations, or UEPs, M1(YAP), M145(P205), M203, P144, P153, P165, P167, P183.

Haplogroup DE is often referred to by the most well-known unique event polymorphism
Unique event polymorphism
In genetic genealogy a unique-event polymorphism is a genetic marker that corresponds to a mutation which is likely to occur so infrequently that it is believed overwhelmingly probable that all the individuals who share the marker, worldwide, will have inherited it from the same common ancestor,...

 (UEP) which defines it, the Y-chromosome Alu Polymorphism
Polymorphism (biology)
Polymorphism in biology occurs when two or more clearly different phenotypes exist in the same population of a species — in other words, the occurrence of more than one form or morph...

 (YAP). The YAP mutation was caused when a strand of DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...

 called Alu
Alu sequence
An Alu element is a short stretch of DNA originally characterized by the action of the Alu restriction endonuclease. Alu elements of different kinds occur in large numbers in primate genomes. In fact, Alu elements are the most abundant mobile elements in the human genome. They are derived from the...

, which copies itself, inserted a copy into the Y chromosome
Y chromosome
The Y chromosome is one of the two sex-determining chromosomes in most mammals, including humans. In mammals, it contains the gene SRY, which triggers testis development if present. The human Y chromosome is composed of about 60 million base pairs...

. A Y chromosome that has the YAP mutation is called YAP-positive (YAP+), and a Y chromosome that does not have the YAP mutation is labeled YAP-negative (YAP-).

Haplogroup DE is an estimated 65,000 years old.

Distribution

The majority of DE male lines can be categorized as being in either Haplogroup D (Y-DNA)
Haplogroup D (Y-DNA)
In human genetics, Haplogroup D is a Y-chromosome haplogroup. Both D and E lineages also exhibit the single-nucleotide polymorphism M168 which is present in all Y-chromosome haplogroups except A and B, as well as the YAP unique-event polymorphism, which is unique to Haplogroup...

, which likely originated in Asia
Asia
Asia is the world's largest and most populous continent, located primarily in the eastern and northern hemispheres. It covers 8.7% of the Earth's total surface area and with approximately 3.879 billion people, it hosts 60% of the world's current human population...

, the only place where it has been found, or haplogroup E
Haplogroup E (Y-DNA)
In human genetics, Haplogroup E is a human Y-chromosome DNA haplogroup. Haplogroup E is one of the two main branches of the older Haplogroup DE, the other main branch being haplogroup D. The E clade is divided into two subclades: E1 and E2 .-Origins:Underhill et al. proposed that haplogroup E...

, which is believed to have originated in East Africa
East Africa
East Africa or Eastern Africa is the easterly region of the African continent, variably defined by geography or geopolitics. In the UN scheme of geographic regions, 19 territories constitute Eastern Africa:...

 or the Near East
Near East
The Near East is a geographical term that covers different countries for geographers, archeologists, and historians, on the one hand, and for political scientists, economists, and journalists, on the other...

. The remainder are said to be in the paragroup DE*, confirmed cases of which are extremely rare.

In a study of over 8000 men worldwide including 1247 Nigeria
Nigeria
Nigeria , officially the Federal Republic of Nigeria, is a federal constitutional republic comprising 36 states and its Federal Capital Territory, Abuja. The country is located in West Africa and shares land borders with the Republic of Benin in the west, Chad and Cameroon in the east, and Niger in...

ns, Haplogroup DE*
* (haplogroup)
Paragroup is a term used in population genetics to describe lineages within a haplogroup that are not defined by any additional unique markers. In human Y-chromosome DNA haplogroups, paragroups are typically represented by an asterisk placed after the main haplogroup...

 was observed in only 5 Nigerian males (5/1247). However, the study's authors caution that "the apparently paraphyletic status of this haplogroup, and hence the conclusions of nested cladistic analysis, are also likely to be illusory" and that "the only genealogically meaningful definition of the age of a clade is the time to its most recent common ancestor, but only if DE* is paraphyletic does it also become automatically older than D or E in this sense." More recently, one example of DE* was found amongst the Nalu
Nalu
Nalu may mean:*Nalu , a people in Guinea-Bissau*Nalu , a drink made by the Coca-Cola company*Nalu , a technology demo by Nvidia, and the name of the main character, a mermaid...

 in Guinea Bissau (1/17). The DE* sequence of this individual differs by one mutation from the DE* sequence of the Nigerian individuals. This indicates common ancestry, though the phylogenetic relationship between the two lineages was not determined in this particular study. A 2008 study detected DE* in two individuals from Tibet
Tibet
Tibet is a plateau region in Asia, north-east of the Himalayas. It is the traditional homeland of the Tibetan people as well as some other ethnic groups such as Monpas, Qiang, and Lhobas, and is now also inhabited by considerable numbers of Han and Hui people...

 (2/594).

Haplogroup DE is found in Africa (Haplogroups E and DE*) and East Asia (Haplogroups D and DE*) but is largely absent in between these two regions. The presence of DE across widely separated regions has confounded investigators trying to reconstruct the migration of humans from Africa to Asia. At some time, there was an extinction of DE lineages in West, South and Central Asia. Autochthonous DE lineages are absent in India, an important region in the dispersal of humans in Asia. However DE lineages have been detected in relict populations of the Andaman Islands
Andaman Islands
The Andaman Islands are a group of Indian Ocean archipelagic islands in the Bay of Bengal between India to the west, and Burma , to the north and east...

. Underhill et al. 2007, suggest the possibility that deleterious mutations in some DE carriers may explain the extinction of DE lineages in India.

The only person in the world to be confirmed in Hg DE* by commercial testing is Ruslan bin Makin Al Bitar, maternal half-brother to Yomal Sidoroff-Biarmskii, who ordered the testing. The Al Bitar family are Sunni Syria
Syria
Syria , officially the Syrian Arab Republic , is a country in Western Asia, bordering Lebanon and the Mediterranean Sea to the West, Turkey to the north, Iraq to the east, Jordan to the south, and Israel to the southwest....

n Arab
Arab
Arab people, also known as Arabs , are a panethnicity primarily living in the Arab world, which is located in Western Asia and North Africa. They are identified as such on one or more of genealogical, linguistic, or cultural grounds, with tribal affiliations, and intra-tribal relationships playing...

s of Damascus
Damascus
Damascus , commonly known in Syria as Al Sham , and as the City of Jasmine , is the capital and the second largest city of Syria after Aleppo, both are part of the country's 14 governorates. In addition to being one of the oldest continuously inhabited cities in the world, Damascus is a major...

, Syria
Syria
Syria , officially the Syrian Arab Republic , is a country in Western Asia, bordering Lebanon and the Mediterranean Sea to the West, Turkey to the north, Iraq to the east, Jordan to the south, and Israel to the southwest....

. In yhrd.org , a similar haplotype was found only in Syrian Arabs of provincial Syria
Syria
Syria , officially the Syrian Arab Republic , is a country in Western Asia, bordering Lebanon and the Mediterranean Sea to the West, Turkey to the north, Iraq to the east, Jordan to the south, and Israel to the southwest....

 from the work "Donbak2006" (9 out of 9 markers, 1 out of 113 individuals). This implies that Syria
Syria
Syria , officially the Syrian Arab Republic , is a country in Western Asia, bordering Lebanon and the Mediterranean Sea to the West, Turkey to the north, Iraq to the east, Jordan to the south, and Israel to the southwest....

 has some small share of Hg DE* (never reported anywhwre outside West Africa
West Africa
West Africa or Western Africa is the westernmost region of the African continent. Geopolitically, the UN definition of Western Africa includes the following 16 countries and an area of approximately 5 million square km:-Flags of West Africa:...

 & Tibet
Tibet
Tibet is a plateau region in Asia, north-east of the Himalayas. It is the traditional homeland of the Tibetan people as well as some other ethnic groups such as Monpas, Qiang, and Lhobas, and is now also inhabited by considerable numbers of Han and Hui people...

 by academic studies). However, all the other studies of Syria
Syria
Syria , officially the Syrian Arab Republic , is a country in Western Asia, bordering Lebanon and the Mediterranean Sea to the West, Turkey to the north, Iraq to the east, Jordan to the south, and Israel to the southwest....

 have yet failed to find this Hg. The only haplotype outside Africa that is anywhere close to the above can be found in the smgf.org database belonging to the Othman family, a Palestinian Arab family of Jerusalem.

Origins

Discovery

The YAP insertion was discovered by scientists led by Michael Hammer of the University of Arizona. Between 1997 and 1998 Hammer published three articles relating to the origins of haplogroup DE. These articles state that YAP insertion occurred in Asia. As recently as 2007, some studies such as Chandrasekar et al. 2007, cite the publications by Hammer when arguing for an Asian origin of the YAP insertion.

The scenarios outlined by Hammer include an out of Africa migration over 100,000 years ago, the YAP+ insertion on an Asian Y-chromosome 55,000 years ago and a back migration of YAP+ from Asia to Africa 31,000 years ago by its subclade haplogroup E. This analysis was based on the fact that older African lineages, such as haplogroups A
Haplogroup A (Y-DNA)
In human genetics, Haplogroup A refers to a group of y-chromosome lineages that were among the first to branch off from the root of the human y-chromosome phylogeny...

 and B
Haplogroup B (Y-DNA)
In human genetics, Haplogroup B is a Y-chromosome haplogroup.-Distribution:Haplogroup B is localized to sub-Saharan Africa, especially to tropical forests of West-Central Africa. After Y-haplogroup A, it is the second oldest and one of the most diverse human Y-haplogroups...

, were YAP negative whereas the younger lineage, haplogroup E
Haplogroup E (Y-DNA)
In human genetics, Haplogroup E is a human Y-chromosome DNA haplogroup. Haplogroup E is one of the two main branches of the older Haplogroup DE, the other main branch being haplogroup D. The E clade is divided into two subclades: E1 and E2 .-Origins:Underhill et al. proposed that haplogroup E...

 was YAP positive. Haplogroup D, which is YAP positive, was clearly an Asian lineage, being found only in East Asia with high frequencies in Japan and Tibet. Because the mutations that define haplogroup E were observed to be in the ancestral state in haplogroup D, and haplogroup D at 55kya, was considerable older than haplogroup E at 31kya, Hammer concluded that haplogroup E was a subclade of haplogroup D.

Contemporary studies

In 2000 a number of scientists had started to reassess the hypothesis of an Asian origin of the YAP insertion. Underhill et al. 2000 identified the D-M174 mutation that defines haplogroup D
Haplogroup D (Y-DNA)
In human genetics, Haplogroup D is a Y-chromosome haplogroup. Both D and E lineages also exhibit the single-nucleotide polymorphism M168 which is present in all Y-chromosome haplogroups except A and B, as well as the YAP unique-event polymorphism, which is unique to Haplogroup...

. The M174 allele is found in the ancestral state in all African lineages including haplogroup E. The discovery of M174 mutation meant that haplogroup E could not be a subclade of haplogroup D. These findings effectively neutralized the argument of an Asian origin of the YAP+ based on the character state of the M40 and M96 mutations that define haplogroup E. According to Underhill et al. 2000, the M174 data alone would support an African origin of the YAP insertion.

Further arguments were made supporting and African origin of the YAP in Underhill et al. 2001. The arguments for an African origin include.
  1. Africa has the highest frequency of YAP(>80%). Whereas the YAP+ in Asia has a fairly restricted geographic distribution, mainly at low to moderate frequencies (average 9.6%) in East Asia.
  2. It was claimed that there was no archaeological evidence of a back-migration to Africa, and at the time of writing that there was no unequivocal Y DNA
    Y chromosome
    The Y chromosome is one of the two sex-determining chromosomes in most mammals, including humans. In mammals, it contains the gene SRY, which triggers testis development if present. The human Y chromosome is composed of about 60 million base pairs...

    , mitochondrial DNA
    Mitochondrial DNA
    Mitochondrial DNA is the DNA located in organelles called mitochondria, structures within eukaryotic cells that convert the chemical energy from food into a form that cells can use, adenosine triphosphate...

     or autosomal DNA evidence of a back migration to Africa.
  3. Although Haplogroup C
    Haplogroup C (Y-DNA)
    In human genetics, Haplogroup C is a Y-chromosome haplogroup, defined by UEPs M130/RPS4Y711, M216, P184, P255, and P260, which are all SNP mutations. It is a sibling clade of Haplogroup F, within the more ancient grouping of Haplogroup CF...

     seems to have originated in Asia at a similar time to Haplogroup DE's origin, Haplogroup C shows no sign of back migration to Africa.


The African origin of the YAP+ is also supported by studies concerning haplogroup E. In Altheide and Hammer 1997, the authors argue that haplogroup E arose in Asia on an ancestral YAP+ allele before migrating back to Africa. However some studies, such as Semino et al., indicate that the highest frequency and diversity of haplogroup E is in Africa, and Africa is the most likely place of origin of the haplogroup.

The models supporting an African origin or an Asian origin of the YAP+ insertion both required the extinction of the ancestral YAP chromosome to explain the current distribution of the YAP+ polymorphism. Paragroup DE* possesses neither the mutations that define haplogroup D or haplogroup E. If paragroup DE* was found in one location but not the other, it would boost one theory of the other. Haplogroup DE* has recently been found in Nigeria
Nigeria
Nigeria , officially the Federal Republic of Nigeria, is a federal constitutional republic comprising 36 states and its Federal Capital Territory, Abuja. The country is located in West Africa and shares land borders with the Republic of Benin in the west, Chad and Cameroon in the east, and Niger in...

, Guinea-Bissau
Guinea-Bissau
The Republic of Guinea-Bissau is a country in West Africa. It is bordered by Senegal to the north, and Guinea to the south and east, with the Atlantic Ocean to its west....

 and also in Tibet
Tibet
Tibet is a plateau region in Asia, north-east of the Himalayas. It is the traditional homeland of the Tibetan people as well as some other ethnic groups such as Monpas, Qiang, and Lhobas, and is now also inhabited by considerable numbers of Han and Hui people...

. The phylogenetic relationship of three DE* sequences has yet to be determined, but it is known that the Guinea Bissau sequences differ from the Nigerian sequences by at least one mutation. Weale et al. state that the discovery of DE* among Nigerians pushes back the date for the most recent common ancestor
Most recent common ancestor
In genetics, the most recent common ancestor of any set of organisms is the most recent individual from which all organisms in the group are directly descended...

 (MRCA) of African YAP chromosomes. This, in his view, has the effect of reducing the time window through which a possible back migration from Asia to Africa could occur.

Chandrasekhar et al. 2007, have argued for the Asian origin of the YAP+. They state,
The presence of the YAP insertion in Northeast Indian tribes and Andaman Islanders with haplogroup D suggests that some of the M168 chromosomes gave rise to the YAP insertion and M174 mutation in South Asia

They also argue that YAP+ migrated back to Africa with other Eurasian haplogroups. These include Haplogroup R1b1
Haplogroup R1b (Y-DNA)
The point of origin of R1b is thought to lie in Eurasia, most likely in Western Asia. T. Karafet et al. estimated the age of R1, the parent of R1b, as 18,500 years before present....

* (18-23kya), which has been observed with especially high frequency among the members of some tribes in northern Cameroon
Cameroon
Cameroon, officially the Republic of Cameroon , is a country in west Central Africa. It is bordered by Nigeria to the west; Chad to the northeast; the Central African Republic to the east; and Equatorial Guinea, Gabon, and the Republic of the Congo to the south. Cameroon's coastline lies on the...

, and Haplogroup T
Haplogroup T (Y-DNA)
In human genetics, Haplogroup T is a human Y-chromosome DNA haplogroup. From 2002 to 2008, it was known as Haplogroup K2. It should not be confused with the mitochondrial DNA haplogroup T, of the same name....

 (25-30kya), which has been observed in low frequencies in Africa. Haplogroup E at 50kya is considerably older than these haplogroups and has been observed at frequencies frequencies of 80-92% in Africa.

In a press release concerning a study by Karafet et al. (2008), Michael Hammer, revised the dates for the origin Haplogroup DE from 55,000 years ago to 65,000 years ago. For haplogroup E, Hammer revised the dates from 31,000 years ago to 50,000 years ago. Hammer is also quoted as saying “The age of haplogroup DE is about 65,000 years, just a bit younger than the other major lineage to leave Africa, which is assumed to be about 70,000 years old,” in which he implies that haplogroup DE left Africa along with Haplogroup CF.

Peter Underhill states that there will always be uncertainty regarding the precise origins of DNA sequence variants such as YAP because of a lack of knowledge concerning prehistoric demographics and population movements. However Underhill contends that with all the available information, the African origin of the YAP+ polymorphism is more parsimonious and more plausible than the Asian origin hypothesis. Other authors who have published or co-published works in support of an African origin the YAP+ include Luigi Luca Cavalli-Sforza
Luigi Luca Cavalli-Sforza
Luigi Luca Cavalli-Sforza is an Italian population geneticist born in Genoa, who has been a professor at Stanford University since 1970 .-Books:...

, Toomas Kivisild
Toomas Kivisild
Toomas Kivisild, is an Estonian geneticist. He graduated in 1992 as a zoologist, and completed his Ph.D. at the Estonian Biocentre research institute. He is a professor of human evolutionary genetics at Cambridge University and his main work has focused on human mtDNA variation.Stephen...

, Spencer Wells
Spencer Wells
Spencer Wells is a geneticist and anthropologist, an at the National Geographic Society, and Frank H.T. Rhodes Class of '56 Professor at Cornell University. He leads The Genographic Project.-Education:...

, Linda Stone and Paul F. Lurquin.

Tree

This phylogenetic tree of para-haplogroup DE is based on the YCC 2008 tree and subsequent published research.
  • DE (M1/YAP, M145 [P205], M203, P144, P153, P165, P167, P183)
    • D
      Haplogroup D (Y-DNA)
      In human genetics, Haplogroup D is a Y-chromosome haplogroup. Both D and E lineages also exhibit the single-nucleotide polymorphism M168 which is present in all Y-chromosome haplogroups except A and B, as well as the YAP unique-event polymorphism, which is unique to Haplogroup...

      (M174, (021355))
    • E
      Haplogroup E (Y-DNA)
      In human genetics, Haplogroup E is a human Y-chromosome DNA haplogroup. Haplogroup E is one of the two main branches of the older Haplogroup DE, the other main branch being haplogroup D. The E clade is divided into two subclades: E1 and E2 .-Origins:Underhill et al. proposed that haplogroup E...

      (SRY4064, M96, P29, P150, P152, P154, P155, P156, P162)
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